options handling change #57
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- contains Boost fix for borken C++11 std::regex on GCC 4.8.x
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DrYak
commented
Nov 20, 2017
| else() | ||
| target_link_libraries(hc BamTools) | ||
| target_link_libraries(hc BamTools docopt_s) |
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NOTE:
I am mimicking the current behaviour where docopt is compiled as an object (docopt.o) straight into
haploclique, no matter what shared/static setting is in action. No external shared object is ever needed.
Here the static docopt library is used no matter what, so that the final haploclique never relies on any lib docopt.so
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@armintoepfer : oops, something is wrong Circleci doesn't even start!? |
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@SoapZA : If you would also like to review this pull. |
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This pull request did also happen to solve this issue regarding using upstream docopt as a submodule (done in this commit ) |
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This branches contains 2 different modifications to haploclique :
docopt
I've replaced the built-in docopt version 0.6.1 with an external git submodule pulling version 0.6.2.
That version contains bugfixes that cause the exceptions thrown to disappear.
It also has an officially supported switch (
-DUSE_BOOST_REGEX) that replace the C++11 std::regex engine with Boost.Regex, for older version like GCC 4.8.x that lack functionnal Regex.help return code
I turned on docopt's support for
--help(and--version) so that now these display the info and return a success exit code (which is a requirement for bioconda recipes'test:sections)